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#ifndef theplu_yat_omic_bam_read_filter |
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#define theplu_yat_omic_bam_read_filter |
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|
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// $Id$ |
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/* |
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Copyright (C) 2013, 2014, 2018, 2020, 2023 Peter Johansson |
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This file is part of the yat library, http://dev.thep.lu.se/yat |
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|
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The yat library is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License as |
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published by the Free Software Foundation; either version 3 of the |
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License, or (at your option) any later version. |
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The yat library is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with yat. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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#include <htslib/sam.h> |
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#include <functional> |
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|
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// this flag was defined in bam.h but has disappeared in htslib |
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#ifndef BAM_DEF_MASK |
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#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) |
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#endif |
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|
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namespace theplu { |
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namespace yat { |
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namespace omic { |
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|
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class BamRead; |
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/** |
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\brief Filter bam reads |
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|
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Class is specifically designed to be used with |
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boost::filter_iterator. The code below for example |
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\code |
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InBamFile in("example.bam"); |
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BamReadIterator begin(in); |
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BamReadIterator end; |
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BamReadFilter filter(20, 0); |
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some_algo(make_filter_iterator(filter, begin, end), |
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make_filter_iterator(filter, end)); |
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\endcode |
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iterates over all read with mapping quality 20 or greater. |
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|
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\since new in yat 0.11 |
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*/ |
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class BamReadFilter |
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{ |
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public: |
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/// Functor takes a const BamRead& |
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typedef const BamRead& argument_type; |
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/// Functor returns \c bool |
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typedef bool result_type; |
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|
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/** |
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Create a functor which accepts reads with mapping quality \a |
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mapQ (or greater), flag must be unset in bits described by a \a |
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filter_flags, and flag must be set in bits described by \a |
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required_flags. |
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*/ |
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BamReadFilter(unsigned char mapQ, unsigned int filtered_flags=BAM_DEF_MASK, |
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unsigned int required_flags=0); |
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|
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/** |
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return true if 1) bam mapping quality is at least mapQ AND 2) |
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bam flags & filter_flags == 0 (no filter bit set) AND 3) bam |
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flags & required_flags == required_flags (all req bits set) |
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*/ |
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bool operator()(const BamRead& bam) const; |
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private: |
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unsigned char mapQ_; |
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unsigned int filtered_; |
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unsigned int required_; |
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}; |
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|
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}}} |
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#endif |